You are saved! The plug cap boot has a spiral wire at the top of the cap. You can 'screw' the cap back onto the wire. In the FSM, under the procedure to check the resistance of the spark plug cap it instructs you to take the wire off the cap. You may want to trim just a tiny bit off of the coil wire to help make a better connection when you screw it back onto the cap.
OK...maybe I'm a little slow on the uptake but when you say "screw" the cap back onto the wire are you saying that I will be pushing the wire back into the boot with a twisting motion? I noticed that there were indentions on the wire so I pushed it back in the boot up to the last one. I had to twist the boot to get it to slide up and then it stopped.
Is there a better way to get the boots off the plugs like some sort of tool with a curved end that will pry them up. There's not a ton of room and with the plumbing and all, i had a hard time getting my fingers on them with enough grip to pull them up.
Push the shortened wire back into the boot, nice and straight. When it stops, twist the cap as if screwing it onto the wire (you are). A little silicone grease will help things along.
There are tools for pulling plug caps, but you wouldn't have much room to use one. Removing all the plumbing and capping off the hose nipples will help, and you don't have to put it back. (AIR Induction Removal)